From: Deepayan Sarkar <deepayan_at_stat.wisc.edu>

Date: Wed 16 Feb 2005 - 02:56:16 EST

R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Wed Feb 16 02:18:30 2005

Date: Wed 16 Feb 2005 - 02:56:16 EST

On Tuesday 15 February 2005 08:15, CG Pettersson wrote:

> Hello all!

*>
**> R2.0.1, W2k
**>
**> I posted this question to the list last Sunday without getting any
**> replies on the list. I got two off the list though, suggesting me to
**> plot "manually" as a second step, from estimable() or intervals()
**> objects respectively. As this was not really what I wished for, I
**> take the risk to upset somebody with a trivial question, and re-post
**> it (just a little edited).
**>
**> So, here it is again:
**>
**> I use lme() from nlme to make mean estimates from series of field
**> experiments where not all treatments (like "variety") are present in
**> all experiments. (An old problem in variety evaluation).
**>
**> A typical call is:
**>
**> yield.lme <- lme(Yield ~ Variety, data = data,
**> na.action = na.omit,
**> random = ~ 1 | Experiment/Block)
**>
**> This works well, even when observations are lacking. I have checked
**> against the accepted method for doing this in Sweden, which is
**> PROC MIXED in SAS, and the fitted fixed effects are more or less
**> identical. I use estimable() from gmodels (gregmisc package) to
**> extract estimates, standard errors and such. I use matrices with the
**> variety names as row names, it works smooth.
**>
**> What I am unable to, as yet, is to make nice plots of the estimates
**> for a given set of varieties. To use only the fixed call directly on
**> the dataset works for many plooting functions, but produces the wrong
**> graphs, as the structure is not used. The structure (the random call)
**> has to be used, as there are NA:s in the dataset.
*

It's not clear to me what you are looking for. In particular, exactly what 'estimates' do you want to plot? Could you give us a reproducible example (preferably using a dataset from nlme) and describe the plot you are looking for in terms of that example?

Deepayan

> Pinheiro & Bates have a lot of graphics on lme objects, but they try

*> to illustrate more sophisticated relations than my need. Iīve looked
**> through gplots and the graphic parts of nlme without any hits.
**> Probably, my difficulties are just due to my own lack of skill. Some
**> standard plotting facility plotting directly from the lme object
**> ought to work, but I donīt understand how.
**>
**> How should I do this?
**>
**> Cheers
**> /CG
*

R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Wed Feb 16 02:18:30 2005

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